Advanced Mind, Compassionate Heart
by Dragonchad
Summary: Naruto unveils a hidden secret from his youth, and loses hope for his dream of becoming Hokage, but he can't give up on helping others, and does his best to give everyone their own happy ending.
1. Chapter 1

Chakra is a mysterious energy, and even though it provides similar, if not the same powers to the shinobi that train with it, it's inherent effects are not always the same. For many, the introduction of chakra gives one the basic abilities that most refer to as Jutsu.

However, some people have strange effects born from chakra in their body, which are generally known as Bloodline Limits. While it is possible for children to be born with a completely new effect, clans and families that have the same or similar bloodlines will breed true, until the majority of the group has the same chakra effects. This is why there are some that are born without the ability, or some with a more powerful version.

A young mind, unable to comprehend its own existence, but conscious enough to breathe and make it's discomfort known, will generally spend most of its unborn life just letting it's mother know of its hunger, and that is it's limit. But for the unborn Naruto Uzumaki, his chakra systems had just developed. This coupled with the massive force of chakra that was sealed just next to him led to his brain being developed exponentially faster.

In other words, his current thought processes were equal to a 3, bordering on 4 year old infant. With a brain that developed, emotions and higher thought levels were well developed, and he tried to learn. His physical capabilities were low, but he didn't have anywhere to move anyway. However, there was something that he was capable of looking at, and investigating.

The Kyuubi's seal.

Naruto was currently 5 months…

With an angry, and finally fully-conscious roar, The Kyuubi launched a massive claw at Naruto's infant body, in an attempt to prevent the sealing. Both of Naruto's parents jumped in the way, and he watched as they gave him their last words and finished the sealing. In a feeble movement, he dipped his fingers in the precious ink that laid the seal bare in his body, and adding a few small characters, nearly invisible among the rest of the seal.

Then his young body forced sleep upon him, and he knew no more.

The third Hokage, recently chosen to retake the mantle as the leader of the village, decided that he should be able to follow tradition with Naruto, and perform a small mental exam to make sure that he was healthy.

However, when Inoichi Yamanaka checked him out, he found a mind that was incredibly developed, the likes of which was never seen before. He warned the Hokage about the complex level of the child's psyche, and left. Grimly, Hiruzen called his student, Jiraiya, to his office, and conveyed the information. Jiraiya, considered to be a seal master, developed a special seal that would lock away the development, and lower his intelligence to a normal level for a baby of less than a week of age. It was applied, and the two of them decided to send him to an orphanage for his wellbeing, due to their inability for either of them to care for a child.


	2. Chapter 2

A young Naruto Uzumaki was walking down the side streets of Konoha, knowing that with his luck, he would meet people on the main roads who would be mean to him, even if it was this late at night, when he heard a noise. It sounded strange, metallic. He decided to go investigate.

He climbed up a nearby wall, and jumped over. He felt a small pain from his ankles, but he ignored it, breathing raggedly from the small exertion.

Gently sneaking out into the bigger roads, he looked around cautiously. He didn't see anyone, so he slowly emerged onto what appeared to be the main street in the area. That is when he noticed two things. 1. This was the Uchiha district, easily noticeable due to the large fans adorning every building, and 2. There were several dead, but still bleeding bodies in the street.

In dawning horror, he turned and ran as fast as possible, not even noticing as he passed a boy his age, who was simply collapsed, and twitching. He ran blindly, visions of blood were all that he could see. He nearly tripped, but recovered just in time to hit something, which managed to actually make him fall.

When he looked up, it was a young man, a teenager of about 13 years. He had a bloodied tanto out, and glowing red eyes with black tomoe. He seemed like he was going to talk to Naruto, but before a word was said, another figure emerged, a man with indiscernible features, with the only noticeable identifier being an orange mask.

The young man, who Naruto finally identified as Crow, the friendly Anbu who would watch over him occasionally, turned to talk with the masked man, only to be instantly decapitated. Naruto's horror was greater than ever before, and he felt paralyzed before he felt a strange falling sensation, and found himself in the depths of a large sewer.

Glancing around in surprise, and still greater fear, he noticed an enormous barred gate, with an eerie darkness on the other side.

"It's you." An ominous and deep voice voiced.

"M-me?" Naruto asked.

"M-me?" the voice mocked. "You sound so pitiful. It's a wonder that I ever felt threatened by such a runt."

Naruto's mind raced, trying to figure out who it was that he could be talking to.

"To think that you, one who had such power before even your birth, would become such a wimpy idiot. You don't even know what you yourself have done, locked away as you are. But alas, without your intelligence, you are just a bore, someone that could be anyone, instead of who you were. Well. Perhaps I should change that." The voice ended ominously as a flash of red overtook Naruto.

Naruto's eyes snapped open, and a slight red tinge appeared on his eyes. Though the chakra that he wielded was small in comparison to even his own, it awakened just enough power for Naruto to feel as if he should attack, instead of run, but the Masked man was already gone. A bestial roar of rage escaped him, and more red chakra enveloped his body. Unbidden, a hidden seal that sealed himself broke down and collapsed, and Naruto's own blue life energy erupted around him. The Kyuubi's chakra was overtaken and drowned in Naruto's own energy, and he felt his thoughts were unimpeded, as they had been once before.

Calculations shot through his mind quickly, and he recalled every book he'd ever had the chance to glance at, and every memory that could allow him to learn, had he been able to remember them before. His newfound intelligence had the effect of granting him Eidetic memory, and he was grateful for that.

Immediately, his decisions in his past made themselves clear, and he discarded them. His idiotic consciousness had wished to be respected? To gain the title of Hokage? How ridiculous. But even with such knowledge, intelligence does not mean a loss of compassion, of empathy. It simply means understanding how much help it will do.

To be truly helpful, you must look at one's suffering as motivation to end all suffering, not to appease the single man.

Naruto realized this now, and he finally understood what would be the best thing for him to do.

A slight fluctuation in his chakra gave it the command he sought, to create a perfect transformation technique, and it succeeded. His body changed shape to become Itachi Uchiha, his chakra created a shell that appeared to be Itachi's, and his eyes flashed red. Carefully, and regretfully, knowing how kind Itachi was, he took out the teen's eyes, and set the body ablaze with a minor fire jutsu after carefully searching his attire.

With Anbu taking care of you from the shadows, even hidden as they were, they could always be glimpsed, and with high level shinobi such as them, it was easy to see them perform useful moves such as his next one, and only the problem of chakra ability or remembrance of the hand seals would prevent a normal man from learning such techniques.

Three Shadow Clones appeared, and quickly sped through the Clan district, gathering scrolls, weapons, and activated Sharingan.

With a breath of wind, Naruto the Genius disappeared, leaving a lone clone to take the title of Naruto the Dobe.

There was much work to be done, and much to fix in this world of War.


	3. Chapter 3

Itachi Uchiha sighed. It had been a little TOO easy to convince several powerful ninja that he was the true Itachi, and even the masked man seemed to accept that he had simply cast a powerful genjutsu. Now he was a missing-nin with an S-rank status, and in a criminal organization set out to capture and extract the bijuu from Jinchuuriki, of which, he was one.

It had only been a few months, but 'Itachi' had finished reading and mastered the scrolls he had collected. He heard rumors of Sasuke, and his well-being, but he ignored them for the most part.

Surprisingly, he signed the Crow contract, and the Crows themselves had no problem with him replacing their previous summoners.

"True, you are not an Uchiha, but we of the Crow clan choose summoners for their heart, and their ability. You have obtained the Sharingan; you have successfully impersonated Itachi, and even summoned me. What's more, you're continuing the work that Itachi himself was planning on, so we support you, young Uzumaki." The large crow ended with what Naruto assumed was a grin.

Besides that, Naruto had spent his time as Itachi reading several books on theory and usage of jutsu of all sorts. Recently, he had rekindled his interest in fuuinjutsu, and applied several more seals on his own body, incorporating them to his Jinchuuriki seal so that even a seal master wouldn't attempt to interfere with them.

He discovered that the Uchiha clan had knowledge of a special clone, named the Blood clone, that was supposed to be perfect for any kind of espionage, but he felt that it could be improved upon. With his growing knowledge of fuuinjutsu, he applied a formula to the new blood clone, strengthening it and ensuring it would leave a true corpse upon its death, and infusing the inactive Jinchuuriki seal with some of the Kyuubi's chakra, to better protect it. He was quite proud of one seal in particular, which made the clone's body depend partially on the Kyuubi's chakra, and so, made it able to withstand its power without dispelling.

He sent the specialized clone out to replace the simple shadow clone he left, with success.

Now, all he had to do was come up with a path to Peace, which is what the majority of people want. Easy.

He was assigned a partner, Kisame Hoshigaki. He set off to meet up with him, but was stopped by Orochimaru. Apparently, the Ex-Konoha nin was determined to get a Sharingan, and his were not only the strongest, but one of the only sets of the doujutsu left. Itachi used a simple (to him) genjutsu to escape, and decided to slit his throat while the man was distracted.

Itachi found some clarity in life as he journeyed with his partner. Their goal was to obtain money for the organization, his role to spy on them, and his personal goal to get stronger and ensure peace. He found some helpful information in Itachi's journal, which he kept on his person. Made sense, he figured. Someone as quiet as Itachi had to vent somehow, and anyone he may have befriended wouldn't have the clearance to know about the Coup.

It described his involvement, and spoke of his decision and hopes for Sasuke to redeem the clan. With the updates he received via Shadow Clone, he knew that Itachi's hope would never come to be, and sought to resolve tensions between the nearly extinct clan and the Village.

First, before Peace could be accomplished between the Hidden Villages, they needed to get rid of the Terrorist organization, which he was now a part of.

A slight sting in his eyes made him aware of the Kyuubi's interference. He slipped into his mindscape.

"Kyuubi." He said, his voice and appearance naturally reverting to his own.

"How dare you wield those cursed eyes!" The beast bellowed.

"Kyuubi. This is not a matter of controlling you, or any Tailed Beast. The Sharingan is a tool, and just so happens to be one that works much better when a giant fox doesn't burn my original genetic code through them. Do you think any Uchiha has Blue eyes?" he replied.

"I refuse to allow you to keep those eyes. No Uchiha can control me!"

"I am no Uchiha, and these eyes are for a part to play. But I understand your discomfort. If you don't want me to use those eyes, then give me something to replace them. Itachi Uchiha is known for his genjutsu, Amaterasu, and Tsukuyomi. Susano'o is supposedly in my reach as well, though I have not used it. If you can make a new eye that has those abilities, even if it can't control a Bijuu, then I will discontinue the Sharingan. Until then, I have no choice."

He left as soon as he finished speaking, refusing to let the beast have the final word.

With a sigh, he performed a jutsu he had created after the first of the Bijuu's tantrums, and absorbed the power of the Sharingan into his eyes from one of the many sets he had kept. This one was from another nondescript Uchiha policeman.

With a burst of chakra, he reactivated his Sharingan, and pushed a little more to activate Mangekyou. A strange design came into existence, a red and black star, with points so thin and many that they were uncountable, swirling as they were. Itachi allowed his eyes to revert to their normal three tomoe state.

Focusing back on his surroundings, Itachi noticed Kisame was talking. He seemed to be reminding Itachi of the new orders. They were to scout out the Kyuubi Jinchuuriki, and if possible, capture him.

His plans were coming together, and all that was left was to discover the last of the secrets of the Uchiha.


	4. Chapter 4

A swirling star, black and red, with immeasurable points, glowed ominously as a blue skinned man swayed slightly. "Itachi" quickly disappeared into the village, headed towards the center of village.

A shunshin had him appearing above the Hokage's office. Before the crows had even finished making his body, he stomped his foot in a specific pattern, clearing the office of Anbu, and he dropped in.

"Itachi?" The Third Hokage asked. "I wasn't expecting to see you here again. Is there important information that you couldn't have Jiraiya relay?"

"The Akatsuki wants us to attempt and take the Kyuubi."

"Well, you could hold off, maybe say that there are too many powerful shinobi around him?"

"A good idea, but I have a better one. I believe that I have managed to figure out their weaknesses enough to eliminate them myself."

The Third Hokage, known as the God of Shinobi, was honestly never more surprised. "C-can you really?"

Itachi only nodded, assured of his skills. He did however, have one last request. "In order to accomplish this, I will need to learn a final jutsu, and my victory will be assured."

"Anything." Responded Hiruzen.

"The Reaper's Death Seal."

The old man paled.

An influx of memories caused Itachi to tense for a moment, and he relaxed again after the information settled into his memories.

With a flourish, the last stroke of his seal was finished, and the brush and ink he was using vanished in his sleeve. Focusing chakra in his index finger, Itachi touched the seal, weaving a small genjutsu to hide the light it created.

Small being a proportional size in this instance, since the fuuinjutsu covered the entirety of the Village Hidden in the Rain.

A fact that was not known to others, but Amegakure is such a small village, that it's shinobi force is entirely a part of Akatsuki, save a few weak Nuke-nin that were given shelter. This information allowed Itachi to form a special seal, which targeted all chakra signatures that were just above civilian level, and absorb the energy from them. The chakra that it absorbed would then fuel another seal that Itachi had interwoven in the first, a special space-time jutsu deterrent seal, preventing the hidden Uchiha's special technique. The only downside is that he could not use his own reality warping jutsu, but just like the true Itachi Uchiha, Naruto would not allow himself to rely on a single technique.

Naruto knew the seal was successfully working when the rain stopped. A black flash was all that signaled his special Shadow Clones. They were created using smaller transformed clones, which were in the shape of crows. The composition of the clones, which used a group Henge to turn into a perfect clone, allowed them to be hit several times, especially using Naruto's special solid transformation.

The clones spread through the city, swiftly dealing death to any collapsed ninja.

In just twenty minutes, and a little ingenuity, Naruto was walking away from a village that was now solely under his power. A simple transformation and some collected samples of the S-rank Nin's blood, and he had the entirety of Akatsuki replaced with his clones, and a lab was in construction to analyze their DNA.

Naruto only had one obstacle left outside of establishing peace between the Nations. Zetsu, the cannibal spy of Akatsuki had managed to escape his slaughter. Of course, his impressive brain power had him anticipate this as well. Naruto chuckled lightly as he walked down a lonesome path. It seems that every ninja he met preferred power to intelligence. His amusement stemmed from the fact that his intelligence gave him the ability to create his own power.

Of course, he thought, his Yin chakra, the mental energy, was incredibly high due to his brain power, and the Kyuubi's Yang chakra sealed away in him had leveled out his reserves, and increased his Yin even more. In a way, he was as powerful as Kyuubi's Yin half by himself, and he would have the full power of the Nine Tails if he were to utilize its chakra.

I suppose I wouldn't have anywhere near my strength if I were not the demon's vessel, he mused.

"But now… I must create a peace that will last." He whispered, a small grin emerging on his face.

The next few weeks would change the world, and Naruto would be the cause of them all.

Naruto Uzumaki-Namikaze. Age 12.

Skill level: SS-rank.

Nin-jutsu: S

Tai-jutsu: B

Gen-jutsu: S

Ken-jutsu: S

Fuuinjutsu: SS

Special Notes: Sharingan. When a Sharingan is swapped, presumably for Eternal Mangekyou, the new eyes will have the design of both eyes if both have Mangekyou. For every Uchiha that was killed, knowing that the Coup was the reason for their demise, nearly every Uchiha unlocked the Mangekyou unknowingly that night. For Naruto, who absorbs the power of each pair of eyes in order to quickly replace missing Sharingan, due to the Kyuubi's interference, he has the effect of adding each Mangekyou to his own. Effects of this occurrence are currently unknown, but Naruto's eyes have evolved to the point of no longer attempting to incorporate new designs, but just adding another uncountable point in his star-like design. His only current Mangekyou abilities that are known are Amaterasu, Tsukuyomi, and possibly Susano'o.

Kyuubi Jinchuuriki.

Chakra defect: Yin overload. Yin chakra is spiritual, and contributes to intelligence and brain power. Naruto developed his Yin chakra months before birth, and the power allowed his mind to develop at ridiculous speeds. This defect is only seen in one other instance, the Nara clan. Their chakra defect provides a Yin-release technique, which increases their intelligence as a side-effect. Due to a lack of Yang chakra, they have lower stamina and imbalanced chakra, leading to the laziness and dependence on their shadow ability.

If this story seems like it's wrapping up quickly, don't you worry. This is going to be a massive crossover, and I just want to get to the next world soon. Honestly, I think Itachi is powerful enough that he could have done this entirely. It doesn't make sense for him not to have killed Orochimaru, or collect, or even burn the Sharingan that the clan members had. Seems like an excuse for Danzo, especially since Itachi is one of the few people besides Naruto who uses the Shadow Clone.

Should post pretty frequently for the next couple days, but I might have to give this laptop back to my friend I'm borrowing it from, so if that happens then I'll be back on by January or February. Ja Ne.


End file.
